This work describes a patterning technique for the photoactive layer of organic photovoltaic modules. We demonstrate the fabrication of efficient poly[3-(hexyl)thiophene-2,5-diyl]:[6,6]-phenyl-C61-butyric acid methyl ester (P3HT:PCBM) based organic photovoltaic modules through a specific surface treatment, based on the deposition of a fluorinated self assembled monolayer (SAM) on top of the bottom electric contact. Direct self-patterning of the photoactive layer is achieved by the high contact angle between the SAM and the polymer solution, while a smooth topography is created by combining two solvents with different surface tensions and boiling points in the polymer:PCBM solution. The resolution of the patterning is approximately 400 lm for modules based on a conventional cell architecture and 120 lm for an inverted architecture. As a result, we show 25 cm2 P3HT:PCBM based organic photovoltaic modules with 10 series-connected cells, fabricated via roll-to-roll compatible deposition and patterning techniques.